Nextflow Registry | nf-core/vardictjava@0.0.0-0c7146d

nf-core/vardictjava @ 0.0.0-0c7146d

The Java port of the VarDict variant caller

variant calling vcf bam snv sv

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

The Java port of the VarDict variant caller

Add the following snippet to your workflow script to include this module.

include { VARDICTJAVA } from 'nf-core/vardictjava'

MIT License

Process

`Name`	`VARDICTJAVA`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bams` file	One or two BAM files. Supply two BAM files to run Vardict in paired mode. `*.bam`
`bais` file	Index/indices of the BAM file(s) `*.bai`
`bed` file	BED with the regions of interest `*.bed`

#2 tuple

`meta2` map	Groovy Map containing fasta information e.g. [ id:'test', single_end:false ]
`fasta` file	FASTA of the reference genome `*.{fa,fasta}`

#3 tuple

`meta3` map	Groovy Map containing fasta information e.g. [ id:'test', single_end:false ]
`fasta_fai` file	The index of the FASTA of the reference genome `*.fai`

Output 4 channels

#1 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.vcf.gz` file	VCF file output `*.vcf.gz`

#2 versions_htslib tuple

`${task.process}` string	The name of the process
`htslib` string	The name of the tool
`tabix -h 2>&1 \| sed -n '2s/Version: *//p'` eval	The expression to obtain the version of the tool

#3 versions_vardictjava tuple

`${task.process}` string	The name of the process
`vardict-java` string	The name of the tool
`realpath \$( command -v vardict-java ) \| sed 's/.java-//;s/-.//'` eval	The expression to obtain the version of the tool

#4 versions_var2vcfvalid tuple

`${task.process}` string	The name of the process
`var2vcf_valid.pl` string	The name of the tool
`var2vcf_valid.pl -h \| sed '2!d;s/.* //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
vardictjava	Java port of the VarDict variant discovery program	https://github.com/AstraZeneca-NGS/VarDictJava

Downloads
Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:21:08 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fvardictjava/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/vardictjava/blobs/sha256:3087e185e116ca15467932a3952943efcf43aebd2335817567a2cc82884e8a57
Size	3.2 KB
Checksum	sha256:3087e185e116ca15467932a3952943efcf43aebd2335817567a2cc82884e8a57